Integrated analysis of single-cell RNA sequencing and bulk transcriptome data identifies a pyroptosis-associated diagnostic model for Parkinson's disease.

Parkinson's disease (PD) is a progressive neurodegenerative disorder characterized by an insidious onset. Despite the emphasis on motor symptom-based diagnosis, there remains an unmet clinical need for effective diagnostic approaches during the prodromal phase of PD. Recent advances in single-cell RNA sequencing (scRNA-seq) and bulk transcriptomic analyses of PD patients open avenues for identifying potential diagnostic biomarkers.

Plasma lipidome, circulating inflammatory proteins, and Parkinson's disease: a Mendelian randomization study.

Background: Observational studies have suggested that plasma lipidome play a pivotal role in the occurrence of Parkinson's disease (PD). However, it remains unknown which lipids among plasma lipidome affect PD and how they exert their influence. Clarity is lacking regarding the causal relationship between plasma lipidome and PD, as well as whether circulating inflammatory proteins serve as mediators.

PCP-bε is a novel positive regulator of pollen germination in Arabidopsis thaliana.

small cysteine-rich peptides play essential roles in different stages of the plant reproductive process. Pollen germination is a prerequisite for double fertilization and is directly related to seed formation and crop yield. However, the small cysteine-rich peptides that are involved in pollen germination remain to be identified.

Risk of Parkinson's disease and depression severity in different populations: A two-sample Mendelian randomization analysis.

Background: Depression is widely recognized as a common non-motor symptom of Parkinson's disease (PD). Across different studies, the reported prevalence of depression in PD varies widely, ranging from 2.7% to 90%, but it is unclear whether this association is due to genetic or acquired factors.

Pseudorabies virus usurps non-muscle myosin heavy chain IIA to dampen viral DNA recognition by cGAS for antagonism of host antiviral innate immunity.

Alphaherpesvirus pseudorabies virus (PRV) causes severe economic losses to the global pig industry and has garnered increasing attention due to its broad host range including humans. PRV has developed a variety of strategies to antagonize host antiviral innate immunity. However, the underlying mechanisms have not been fully elucidated.

Causal role of myeloid cells in Parkinson's disease: Mendelian randomization study.

Background: Previous studies have observed elevated myeloid cells in the peripheral blood of patients with Parkinson's disease (PD), but the causal relationship between them remains to be elucidated. We investigated whether there is a causal relationship between different subtypes of peripheral blood myeloid cells and PD using Mendelian randomization (MR) combined with bioinformatics analysis. Exploring the etiology of PD from the perspective of genetics can remove confounding factors and provide a more reliable theoretical basis for elucidating the pathogenesis of PD.

Exploring the causal relationship between B lymphocytes and Parkinson's disease: a bidirectional, two-sample Mendelian randomization study.

Parkinson's disease (PD) is a neurodegenerative disorder with extensive involvement of motor symptoms, imposing a heavy economic burden on patients and society. B lymphocytes, a group of immune cells associated with humoral immunity, have been shown to be involved in the pathogenesis of PD. However, the causal relationship and potential pathogenic effects of B cell in PD remain unclear.

Identification of key genes and signaling pathways associated with dementia with Lewy bodies and Parkinson's disease dementia using bioinformatics.

Objective: Dementia with Lewy bodies (DLB) and Parkinson's disease dementia (PDD) are collectively known as Lewy body dementia (LBD). Considering the heterogeneous nature of LBD and the different constellations of symptoms with which patients can present, the exact molecular mechanism underlying the differences between these two isoforms is still unknown. Therefore, this study aimed to explore the biomarkers and potential mechanisms that distinguish between PDD and DLB.

CSF α-Synuclein and Tau as Biomarkers for Dementia With Lewy Bodies: A Systematic Review and Meta-analysis.

Objective: This study investigated whether α-synuclein and tau in cerebrospinal fluid (CSF) can be used as biomarkers to diagnose dementia with Lewy bodies (DLB).

Materials And Methods: We retrieved 3303 studies with "Dementia with Lewy bodies," "α-synuclein," and "tau" as keywords. We formulated screening criteria, and 2 researchers completed the screening, quality evaluation, and data extraction tasks.

CD20-positive subcutaneous panniculitis-like T-cell lymphoma presenting as polycranial neuropathy: A CARE-compliant case report and literature review.

Background: Subcutaneous panniculitis-like T-cell lymphoma(SPTCL) is a very rare cytotoxic T-cell skin lymphoma involving subcutaneous tissue, and mainly affects young females. T-cell phenotype is characterized by CD3+, CD8+, and CD4-. SPTCT with polycranial neuropathy has rarely been described.

Effect of GBA gene variants on clinical characteristics of dementia with Lewy bodies: a review and meta-analyses.

Objectives: Glucocerebrosidase (GBA) gene may be a risk factor for dementia with Lewy bodies (DLB). However, due to the small number of existing studies and the small sample size of previous investigations, it is necessary to conduct objective and quantitative analyses of the association between GBA variants and DLB. There is no consensus regarding the relationship between GBA and the clinical characteristics of DLB.

Influence of N6-Methyladenosine Modification Gene HNRNPC on Cell Phenotype in Parkinson's Disease.

This study aimed to explore the N6-methyladenosine (m6A) modification genes involved in the pathogenesis of Parkinson's disease (PD) through data analysis of the two data sets GSE120306 and GSE22491 in the GEO database and further explore its influence on cell phenotype in PD. We analyzed the differentially expressed genes and function enrichment analysis of the two sets of data and found that the expression of the m6A-modification gene was significantly downregulated in the PD group, and it played an important role in DNA metabolism, RNA metabolism, and RNA processing and may be involved in PD. Then, we constructed the differential expression cell line to study the role of this gene in the pathogenesis of PD.

Quantitative assessment of the effect of FGF20 rs1721100 and rs12720208 variant on the risk of sporadic Parkinson's disease: a meta-analysis.

Objectives: While many studies have investigated the associations between fibroblast growth factor 20 (FGF20) rs1721100 (C/G) and rs12720208 (C/T) polymorphisms and susceptibility to Parkinson's disease (PD), their results are controversial. Our present meta-analysis estimated the overall association between FGF20 rs1721100 and rs12720208 polymorphisms and the risk of sporadic PD.

Methods: We performed a comprehensive literature search of the PubMed, Web of Science, Embase, Chinese National Knowledge Infrastructure, and Wanfang Medicine electronic databases, which was updated in April 2021.

Identification of Potential Core Genes in Parkinson's Disease Using Bioinformatics Analysis.

Purpose: This study aimed to explore new core genes related to the occurrence of Parkinson's disease (PD) and core genes that can lead to the progression of PD.

Methods: The expression profile data of GSE42966, which contained six substantia nigra tissues isolated from normal individuals and nine substantia nigra tissues isolated from patients with PD, were obtained from Gene Expression Omnibus. Differentially expressed genes (DEGs) were identified, followed by functional enrichment analysis and protein-protein interaction (PPI) network construction.

The Genetic Architecture of a Congenital Heart Defect Is Related to Its Fitness Cost.

In newborns, severe congenital heart defects are rarer than mild ones. This epidemiological relationship between heart defect severity and incidence lacks explanation. Here, an analysis of ~10,000 mice from two inbred strain crosses illustrates the fundamental role of epistasis.

[Progress in pathophysiology and integrated traditional Chinese and Western medicine of post-intensive care syndrome].

With the continuous improvement of treatment ability in intensive care unit (ICU), many critically ill and complex patients have survived due to the development of technology. However, most of them suffer from the psychological and physiological problems of post-intensive care syndrome (PICS). Therefore, the early identification and prevention of PICS is particularly critical.

A Highly Proliferative Group IIC Intron from Geobacillus stearothermophilus Reveals New Features of Group II Intron Mobility and Splicing.

The thermostable Geobacillus stearothermophilus GsI-IIC intron is among the few bacterial group II introns found to proliferate to high copy number in its host genome. Here, we developed a bacterial genetic assay for retrohoming and biochemical assays for protein-dependent and self-splicing of GsI-IIC. We found that GsI-IIC, like other group IIC introns, retrohomes into sites having a 5'-exon DNA hairpin, typically from a bacterial transcription terminator, followed by short intron-binding sequences (IBSs) recognized by base pairing of exon-binding sequences (EBSs) in the intron RNA.

Broad role for YBX1 in defining the small noncoding RNA composition of exosomes.

RNA is secreted from cells enclosed within extracellular vesicles (EVs). Defining the RNA composition of EVs is challenging due to their coisolation with contaminants, lack of knowledge of the mechanisms of RNA sorting into EVs, and limitations of conventional RNA-sequencing methods. Here we present our observations using thermostable group II intron reverse transcriptase sequencing (TGIRT-seq) to characterize the RNA extracted from HEK293T cell EVs isolated by flotation gradient ultracentrifugation and from exosomes containing the tetraspanin CD63 further purified from the gradient fractions by immunoisolation.

Transgenerational cardiology: One way to a baby's heart is through the mother.

Despite decades of progress, congenital heart disease remains a major cause of mortality and suffering in children and young adults. Prevention would be ideal, but formidable biological and technical hurdles face any intervention that seeks to target the main causes, genetic mutations in the embryo. Other factors, however, significantly modify the total risk in individuals who carry mutations.

Codon identity regulates mRNA stability and translation efficiency during the maternal-to-zygotic transition.

Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal-to-zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by post-transcriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs, this pathway does not fully explain mRNA clearance.

RNA-seq of human reference RNA samples using a thermostable group II intron reverse transcriptase.

Next-generation RNA sequencing (RNA-seq) has revolutionized our ability to analyze transcriptomes. Current RNA-seq methods are highly reproducible, but each has biases resulting from different modes of RNA sample preparation, reverse transcription, and adapter addition, leading to variability between methods. Moreover, the transcriptome cannot be profiled comprehensively because highly structured RNAs, such as tRNAs and snoRNAs, are refractory to conventional RNA-seq methods.

High-throughput sequencing of human plasma RNA by using thermostable group II intron reverse transcriptases.

Next-generation RNA-sequencing (RNA-seq) has revolutionized transcriptome profiling, gene expression analysis, and RNA-based diagnostics. Here, we developed a new RNA-seq method that exploits thermostable group II intron reverse transcriptases (TGIRTs) and used it to profile human plasma RNAs. TGIRTs have higher thermostability, processivity, and fidelity than conventional reverse transcriptases, plus a novel template-switching activity that can efficiently attach RNA-seq adapters to target RNA sequences without RNA ligation.

Efficient and quantitative high-throughput tRNA sequencing.

Despite its biological importance, tRNA has not been adequately sequenced by standard methods because of its abundant post-transcriptional modifications and stable structure, which interfere with cDNA synthesis. We achieved efficient and quantitative tRNA sequencing in HEK293T cells by using engineered demethylases to remove base methylations and a highly processive thermostable group II intron reverse transcriptase to overcome these obstacles. Our method, DM-tRNA-seq, should be applicable to investigations of tRNA in all organisms.

Protein synthesis. Rqc2p and 60S ribosomal subunits mediate mRNA-independent elongation of nascent chains.

In Eukarya, stalled translation induces 40S dissociation and recruitment of the ribosome quality control complex (RQC) to the 60S subunit, which mediates nascent chain degradation. Here we report cryo-electron microscopy structures revealing that the RQC components Rqc2p (YPL009C/Tae2) and Ltn1p (YMR247C/Rkr1) bind to the 60S subunit at sites exposed after 40S dissociation, placing the Ltn1p RING (Really Interesting New Gene) domain near the exit channel and Rqc2p over the P-site transfer RNA (tRNA). We further demonstrate that Rqc2p recruits alanine- and threonine-charged tRNA to the A site and directs the elongation of nascent chains independently of mRNA or 40S subunits.

Broad and adaptable RNA structure recognition by the human interferon-induced tetratricopeptide repeat protein IFIT5.

Interferon (IFN) responses play key roles in cellular defense against pathogens. Highly expressed IFN-induced proteins with tetratricopeptide repeats (IFITs) are proposed to function as RNA binding proteins, but the RNA binding and discrimination specificities of IFIT proteins remain unclear. Here we show that human IFIT5 has comparable affinity for RNAs with diverse phosphate-containing 5'-ends, excluding the higher eukaryotic mRNA cap.